Heart of the Machine
by NinjaLayor
Summary: Dalton never thought that he'd be chosen by one of the mechanical Pokemon that live in his city to be it's partner. Now, Dalton and his friends must discover why the 3 Pokemon, considered gods thanks to technology, vanished, without a trace. If they don't, the world might end at the paws of a group bent on awakening one of the trio's most destructive creations.
1. Prologue

**A/N: I do not own Pokemon. If I did, I'd probably not be writing this as a fan fiction, rather, this would be part of the actual arcs. I don't own Lux, or Merlin, either. Those belong to those two, and I'd like to thank them for being the inspiration that those two are. This is my second attempt at a fanfic, and I'm going to sideboard _Nightfur: Memories Awakened, _as I think that this is going to be something that I'll like working on more, for now (and I need more plot in the other one). I hope that you guys, the readers, enjoy this.**

* * *

A Glaceon sat in a chair, in front of a large table. He looked at the two Lucario sitting at the other two edges, goggles covering his blind eyes. The one on the right was covered in clothing, not a trace of his fur visible, the other... well, looking like a normal Lucario. He lifted his left fore-paw, touching the steel gray metal cuff that was around his neck, before resting it on the table. He cleared his throat, and began to speak. "You two probably wonder why I've called you here. I know you both are very busy with projects, but what I have to say is too important for it to go unheard."

Both of the Lucario looked at the Glaceon, then at each other. Finally, the one on the left spoke up. "Nightfur. We know that you've had issues with things, but I don't think it warrants calling us to your tower."

"If you are done, Merlin, I'll continue," the Glaceon, Nightfur, replied calmly. "I fear that we have put the world in danger. Not immanent danger, mind you, but you do realize that, for the most part, we won't be here forever." Nightfur turned his head to the Lucario to his right. "But then again... you do seem to have a habit of ignoring the laws of time, Lux. Regardless, I am proposing that we make preparations, to preserve ourselves, so that when someone does come, and abuses the technology that we've developed, we'll be there to stop them. I've already begun finalizing my plans, I expect you to do so as well."

Merlin and Lux looked at Nightfur. In unison, they asked the question on both their minds. "What would your plans be?"

Nightfur's voice takes on a tone of finality. "Well, since I am no longer a Lucario, like you two, but a Glaceon, I'm actually at an advantage. I intend on freezing myself, remaining here, frozen, until time comes when I am needed. At that point, Mnementh will thaw me." Nightfur looked at the two once more. "I trust you to make your plans, and I leave you a gift in farewell." He motioned at the two small packages in front of the two. "Those are designed to alert us when one of us awakens, so that the other two might awaken as well." Nightfur smiles, and leaps out of the chair, almost as tall as he is. "Take care you two. I hope to see you both, if my worry is misplaced."

* * *

Five days later, Nightfur sat in front of a window, for one last look at the beautiful landscape surrounding his tower. _When I awake... what will await me?_

Mnementh chittered behind him, bringing back to reality. [_You are ready, are you not?_]

"Yes... I'm ready. Let's go to the command room."

In the command room, Nightfur began to switch the entire tower into emergency mode, powering down all but the critical systems in the tower, and leaving only the emergency lights on. Sighing, he took off the goggles, and gave them to Mnementh, the goggles reforming into the second set of eyes he had, but rarely used. Nightfur began to chill his body, and the air around him became extremely dense. Taking one last breath, he focused, and the air around froze suddenly, encasing him in a six inch layer of ice.

That would be the last breath he would take in two thousand years.

**A/N: A whole new adventure... and we won't even be following Nightfur for a good while. Well, see you with some new work in a while!**


	2. Chapter 1: Meeting Dalton

**A/N: I don't own Pokémon. Otherwise, I wouldn't be using a Windows 95 computer instead of a RAM card. Leave a review if you like, dislike, or whatever, about the story so far. Seriously. Do it. If you are viewing as a guest, please sign up, and leave a review, so that I don't have to worry about there only being 5 guest reviews holding it up for others.**

* * *

If only I had knew what I was getting myself into. I might have never accepted the partnership with one of the mechanical Pokemon that wander Treasure Town... well, what was formally called Treasure Town. Now it's called Treasure City. It's quite large, in fact. It almost covers the entire coastline, and goes back about a mile inland, with large buildings. I have to say, it's quite impressive, to look up from town center to see the tops of massive skyscrapers, built by teams of Pokemon and their robotic companions.

Sorry, I got distracted... I tend to do that a lot these days, ever since, well, that happened. I'll start from the beginning. My name's Dalton. I'm what you'd call an Eevee. I'm nothing special, I look like all my cousins, my sister, and... well, according to my parents, like them when they were kids. I attend one of the oldest, and smallest, schools in the city, Historic Academy. They say that one of the most famous exploration guilds in history was built there, and that it's an honor to go to a school built on such a historic site. That's a bunch of lies. At least the part of it being an honor. The school is basically a holding tank for those who haven't ended partnering up with one of the mechanical Pokemon that live in the city.

You know, it wasn't until this whole mess that the origin of those mechanical Pokemon was a complete mystery. They just showed up about one thousand years ago, as one massive group. They had no memory of their creators, or where they came from. It actually took about fifty more years before we could actually understand them, since they weren't capable of PokeSpeech. They still aren't. We had developed microchips meant to be implanted in a Pokemon, able to recall a Pokemon to a location that they set as home after being implanted, similar to the badges that the exploration teams used to carry. It took fifty years to modify them so that it translated what sounds they made into PokeSpeech when we heard it. Shortly after that, they started choosing Pokemon, following the Pokemon they chose everywhere. It was determined that they formed some sort of relationship with the Pokemon they chose, learning from and protecting them. Anyhow, over the last two hundred years or so, it's become a right of passage to form a lifelong partnership with one of the mechanical Pokemon. When we could finally understand them, and ask them about where they came from, all they were able to tell us was that the scorpion was their father. All those historians, most of which came from the Historic Academy, couldn't find any record of a mechanical scorpion in history.

I did it again. Sorry... I can't help it, getting on tangents like that. I attend Historic Academy, or No Tech Tech, as the students at the Institute for Robotics and Technology, our school rival, call us. I have a brother there... I don't see him, since those that attend there board with their mechanical partners. Sorry. Must. Stay focused. Historic doesn't have classes on technology and the like, but rather, we focus on stuff like history, of course, battle methods, and my personal favorite, mythology. So those who attend there are pretty much cut out to be historians, archeologists, and interestingly enough explorers, following the tradition of the old exploration teams.

I guess that I was expecting it to be a normal week at school. Well, in light of all that's happened... I guess I was proven wrong. And I'm glad for it.

* * *

**A/N: I've decided to write this story in a 3rd person point of view. However, there will be certain chapters, such as this, where I'll introduce a character and what their reaction was to the events surrounding the time that I inject their chapter. So, yeah, internet troubles and such delayed this, but I'll see you with the next chapter!  
**

**Update: I'm having trouble coming up with names for professors at Historic Academy! Submit names in the reviews, and I hope to finish the second chapter before the 18th... man, school is closing in on me.**


	3. Chapter 2: For Whom the Bell Tolls

**A/N: I don't own Pokemon. Otherwise, I'd have a PC that could play MechWarrior Online. And some of the most modded Minecraft in existence simultaneously at 300+ FPS. Thanks for the feedback, the chapters will start getting longer now that stuff is actually going to happen. **

* * *

Dalton groaned, the buzzing of a clock bringing him painfully out of the wonder of sleep. There was a rustle of motion, and his ear twitched in annoyance. Suddenly, his sister came flying into his room, and leaped on top of him. He rolled over, trying to fall back asleep. However, that's when Lydia, his sister, began shouting.

"Dalton! Wake up! We've got to get to school!"

"Lydia, please. Five more minutes."

"Dalton! We don't have five more minutes! We're going to be late!"

Dalton jolted awake with that. If there was one thing that he didn't want, it was to be late for his first class this semester. Hind legs kicking off his blanket, he scrambled off of his bed, getting to his paws. He looked at the clock, and to his horror, his sister was right. They had ten minutes before the first classes start, barely enough time to get to the school. He darted quickly to the door, grabbing with his mouth the brown sack containing his lunch. The door sensed the chip implanted near the base of Dalton's skull, and slid open with a quiet hiss of hydraulics releasing pressure. He turned his head, shouting to his sister, between the sack in his mouth. "Let's hurry!" He took off, ears near flat against his back. From what he could hear, his little sister was hot on his heels, trying to keep up with him. Instead of taking the elevator like normal, he went directly to the stairwell, leaping onto the rail, sliding down it. He managed to reach the first floor in ten seconds flat. He looked up, to see his sister about halfway down the third flight of stairs. He set his sack down, and called up to her. "Jump up on the rail! I'll catch you if you fall!"

"Are you crazy? I'm not doing that."

"Well, we're going to be late then."

"Fine." Lydia leaped up onto the rail, and began to slide down. When she reached the bottom, she tried to slow down, to no avail. Falling off the end, she crashed into her brother, ending up on top of him. "Well, you were right. You did catch me."

"Come on! We managed to buy about a minute! Let's hurry!"

The duo raced through the lobby of the apartment building, lunches in hand... or mouth, in this case, out into the bustling streets. Avoiding feet and legs of other Pokemon, mechanical and otherwise, they managed to reach Historic Academy. By the time they had stowed their lunches in the storeroom, the bell began to ring. They managed to dart into their respective classes, just as the bell ended.

Dalton looked around at the classroom. There were the familiar faces from last term, as well as several new ones. His closest friend, Timothy, a Chespin, was sitting with an empty desk beside him. Dalton calmly walked to the desk, and sat down, slightly ashamed of almost being late. He looked up to the front of the room, where the teacher, a Metagross, stood, silently waiting.

"Now that you're here, Mr. Dalton, I'll introduce myself. I am Newton, though I expect you all to call me Professor during this term. Now, can any of you explain the mathematical theory behind the equation behind me, and what it's used for?"

* * *

Four hours later, Lydia, Timothy, Dalton, and another friend of theirs, a Riolu named Hira, were in the cafeteria, eating their lunch while discussing how classes were so far, and what teachers they had. Dalton started naming off a few. "Professor Newton, the maths teacher, is difficult, Battling Technique with Coach is what it always was, though I've noticed it's gotten even harder for me. I can't wait to have Mythology with Mr. Æthin again." Mr. Æthin was a Jolteon, and well versed in all sorts of legends and stories. It was common rumor that Mr. Æthin was the descendent of a famous explorer from long ago, and that he was forced to memorize those legends by his parents at only a few hours old.

Hira mumbled something, around a mouthful of food. Swallowing, she repeated what she had said. "He's got a new book for our class to go over. Some of the illustrations of the Legendary Pokemon were quite detailed." She smiled, pulling out an apple, before devouring it. "I just can't wait for the school battling tournament. You know how I always enjoy trying out for the team... maybe this term we'll beat those jerks at IRT."

Timothy nodded in agreement. "Hey, Dalton. You should try out this year." Hira and Lydia laughed at Dalton's dismayed face.

"No no no no no... I'm not going to sign up for the battling tournament. I'd do anything, if I could avoid signing up for that." Dalton's ears drooped low over his face. "You know I'm no good fighting. Don't even joke about it. Please."

Timothy put a hand on Dalton's head, ruffling the fur. "Okay. I won't." The bell for the end of lunch rang, and the foursome stood, going to the storerooms for their books.

* * *

Two more hours, then it was finally the last class of the day. Dalton carried, in his mouth, a leather strip wrapped around his textbook, letting him carry it without too much difficultly. When he entered the room, he was quite surprised to see not a Jolteon, but rather, a Zoroark, sitting behind the desk at the front of the room. "Who are you?"

The Zoroark smiled kindly. "If you would please take a seat, Dalton, I'll explain to the rest of the class." Dalton did as she told him. The bell for classes to resume rang, and she cleared her throat. "I regret to inform you that Æthin, your Mythology teacher, has decided to take an extended leave of absence, starting at lunch. I have been brought in to teach you Mythology. My name is Mist. I expect you all to call me by that name. Now that pleasantries are out of the way, would someone be so kind enough to tell me where you stopped at the end of last term?"

Dalton cleared his throat, speaking up. "We were beginning to analyze the possibility of the accounts of the Lucario Ironpaw, about the items called Time Gears, and whether or not it was possible for the Legendary Pokemon Darkrai to sabotage the flow of time."

Mist looked at Dalton impressed. "Well done. However, I think I'll give you a break from those accounts. Would you all turn to the final chapter of your textbooks, and I'll get started."

Dalton flipped the pages of his book carefully. Upon reaching the chapter, he looked confused, as did several other students. One of the students raised a paw. "Mist, why are we looking at newer myths? They're not going to be on the final exam, according to Mr. Æthin."

Mist smiles. "You are right. They aren't going to be on the finals. However, there is one trio of Pokemon that I'd like to cover. Who here has heard of the Technology Trio?" No one raised their hands, paws, or other appendages in response. Frowning, Mist continued. "Okay then. The Technology Trio was a group of three Lucario, said to live about two thousand years ago."

Someone in the back of the class raised a paw. "If they are Lucario, why are they even in this book? Mythology deals with Pokemon considered gods. Why them?"

"They were considered gods. Through technology, each one of them managed to achieve different goals. One of the Lucario, named Lux, managed to unlock the secrets of time and space, able to visit different universes. The second, Merlin, created giant, living vehicles, similar to Pokemon. There is an artist rendition of what the Fenris, a Mightyena shaped machine, might have looked like on the fifth page of the chapter. Finally, there was Nightfur. Some say he was part machine himself, others dismiss that as an inaccuracy in documents. A small group of historians actually believe that he died, though somehow came back to life. This Lucario developed machines and technologies, with the goal of aiding both Pokemon and the human race. All three vanished, not a record of their deaths in existence. Now, I want you to analyze this legend, and see what truths you might be able to establish in this."

Dalton thought over what she said. Raising a paw, he spoke up. "The microchips that each Pokemon has implanted in them at hatching these days... they seem to fit with the concept of Lux being able to travel across time and space, while also with the thought that Nightfur was part machine."

Mist nods. "Good. Now, is there anything you think that might contradict this evidence?"

A Fletchling, sitting in the front row of the class, raised up a wing. "No Pokemon has come back to life, without intervention of a greater Legendary Pokemon. So the theory that Nightfur died is out of the question. And several of the recordings of the Technology Trio come from Ironpaw, and we can't be sure about this as several other records by him are still under question."

Mist clapped her paws together. "Well done. You found the link I was hoping you'd find. Several of the accounts about the Trio are from Ironpaw. We know of his writings on encounters of Legendary Pokemon such as Dialga, Palkia, Darkrai, and Cresselia. For one Pokemon to meet so many Legendaries, it throws everything into question." The bell for the end of the school day rang. Mist called out as the students started to stand, heading for the door. "I want a page long paper discussing your view point on the myth of the Technology Trio, with supporting evidence by the end of next week. Enjoy the rest of your day."

The students filled out. Dalton remained sitting there, looking at his book. He finally looked up. "Mist... do you think there is any validity to this legend?"

"Of course. There is always truth in legends, no matter how deeply buried. Besides... I'm related to Nightfur, if my family history is correct."

Dalton sighed, before fitting the leather strap around his book. He started to walk out the door, when Mist spoke up. "How's your mother handling your brother being moved to IRT?" Dalton looked surprised at this.

"She's getting along fine... but how do you know so much about me and my family?"

"I'm not just related to Nightfur, you know. Do you remember that family reunion your father had?"

Dalton shakes his head. "I'm sorry... I don't. I'll ask about it when I get home. See you tomorrow, Mist."

Mist watched Dalton walk out of the classroom. _If only he knew just how much the legends were related to him... he'd believe more._

* * *

Dalton and Lydia walked home, discussing the work they'd have to do. Dalton kept having the nagging feeling that he was being watched or followed, though each time he glanced over his shoulder, there was no one there. As he walked into the lobby of the apartment building that he lived in, he looked over his shoulder for the last time.

He didn't see the shape of the mechanical Combusken as it slipped into the shadows.

**A/N: Well... that took longer than I thought it would. Æthin is not the same Æthin from Nightfur: Memories Awoken. I ran out of ideas, so I just pulled one of my OC names from a metaphorical hat. I'm still in need of names, so please send them in with your reviews. I've got school approaching, so I might have to put this on hold... though I will try to work on this. Gosh... I'm tired. I probably shouldn't have stayed up to watch the first two Transformers movies... well, see you guy's later, and I'll get some sleep.**


	4. Chapter 3: Family Matters

**A/N: Oh my... it's been too long since I had a chance to work on this. Between school, cross country (I run 9th Varsity... and it's only my first year on the team), roleplaying with my friend Axe, more school, and writing for Arctic Fox72's _Pokemon: Shadowed Destiny_, I haven't had any time to work on this. Well, I'm back, so time to get started and back into the groove.**

* * *

Dalton poured over the mythology book, before adding a few more footprint runes to his paper. Setting it out so that the ink would dry, he padded into the living room of the apartment that his family owned. Sighing, he sat down, before triggering the television, watching the news for a brief moment, before looking up at the clock mounted on the wall. "Another hour before Mom and Dad get home from work..." Standing back up, he padded to the door of Lydia's room. "I'm going to go to the park. I'll be back before Mom and Dad get back."

Lydia poked her head back out, a frown on her face. "You better be back before then. You've gotten in enough trouble with Mom and Dad in the past getting home late."

"I'll be back before you can say the word 'mythology' thrice." Dalton dashed off, before his sister could reply, the door closing behind him. He walked up to the elevator, and hit the button closer to the ground to call it with his paw. When it arrived, he climbed in, sitting in the corner silently, looking up at some of the taller Pokemon in the lift. After the lift ground to a halt, and everyone got off, he stood, walking out of the building calmly, and turning left down the street, bustling with Pokemon of all shapes and sizes. After avoiding being trampled by a Gallade and several other Pokemon, he arrived at the gate of the park.

Looking around, he made sure he wasn't being followed, and he went deep into the wooded center of the park, to a small circle of trees, where he curled up, listening to the natural sounds of the forest, amidst the bustling city. A rustling in the bushes disturbed him, and he quickly stood, taking on a defensive stance, expecting something or someone. Hira poked her head out of the bushes, smiling. "I knew I'd find you here!"

Dalton calmed down instantly. "Why did you have to scare me like that? I thought that you could have been some thug planning on attacking me for some reason I can't guess."

"Come on, Dalton. Don't be so negative. You know that the police would be onto a Pokemon like that in a heartbeat, thanks to those microchips that we have implanted. If you were in trouble, they would know where to find you, and if you were seriously hurt."

Dalton sighed. "True... now get on this side of that bush, before you let anyone else know about this little grove. I don't like it when people know about 'my' retreat." Dalton's eyes glistened with memories, from years ago.

* * *

Dalton, much younger than before, stumbled in the direction of the grove, bruised and battered after a hard day at school, which ended with a test on battling against a fellow classmate. He ended up paired with a Riolu, which was bad enough. What irked him was that it was a girl that pummeled him into the sand covered floor of the arena. Pushing his way through the bushes, he was shocked by the sight of that same Riolu sitting in the center of the little grove, back facing him. He started to back away, when she spoke. "You did well... I'm sorry if I hurt you during the test. And how did you know I would be here?"

Dalton was taken aback. "I... I didn't. How did you find this place? I thought I was the only one that knew about it."

The Riolu turned around, a faint smile playing on her lips. "I thought the exact same thing. I found this place a long time ago... I've visited it ever since, when I can in the mornings."

He tilted his head, thinking. "I found this place a while back. I've visited it in the afternoons. I guess you and I've been using this place as a small retreat for a while now."

The Riolu stood, walking over to Dalton. "My name's Hira. What's yours?"

* * *

"'Your' retreat?"

"Fine... our retreat. Anyway... did you hear what happened to Mr. Æthin?"

Hira tilted her head, interested. "No... I didn't. What happened to him?"

Dalton stopped for a second, looking at her. A single thought raced through his mind. _She looks so cute when she... wait, what am I thinking?!_ Shaking his head to clear the thought, he answered. "He took an extended leave of absence, starting in the middle of the school day. That doesn't sound like him, right?"

Hira was taken aback when she heard that. "He did? That's not like him at all. Who taught Mythology after lunch then?"

"There was a Zoroark there named Mist... she seemed nice, even if she did somehow know about my family, especially my brother going to IRT..."

"Creepy..."

"Yeah." Dalton looked upwards towards the sky, and started when he saw how low the sun was. "Oh no... My parents are going to be home any minute now."

"Just activate the recall function of the chip that's implanted in the back of your neck. Even," she added, as Dalton began to open his mouth in protest, "if you don't like the thought of vanishing here and reappearing elsewhere."

Sighing, Dalton nodded, and thinking of home, he activated the chip's function. There was a blinding flash of light, and Hira was left standing there alone in the grove. Dalton's vision cleared, and he was standing there, in his room... with his mother, a Sylveon, and his father, an extremely rare Eeveelution called a Nimbeon, standing there waiting for him. Timidly, Dalton smiled, and greeted his parents. "Hi Mom, hi Dad. Welcome back..."

Dalton's father looked at him sternly. "Son, where were you?"

"I was... at my hidden place."

"You were not at home, like you were supposed to be. Dalton, I'd like to hear you out, but you're spending too much time at this hidden place of yours. Until you tell us where you where you were, you're going to be grounded. We wish we didn't have to do this, but we don't have any other choice... We don't want you getting mixed up in any of those gangs."

Dalton's expression changed, becoming more crestfallen and somewhat indigent. "I was at the park... All that I've done is go to this clearing..."

"Son, you're grounded."

"But Dad..."

Dalton's father had turned, and was half way out of the room. Stopping for a moment, his father looked over his shoulder. "But nothing. For the next week, you're going to school, then coming straight home, to finish your school work."

Dalton buried his face in the plume of fur around his neck, just wanting to vanish then and there. His mother padded over to his side, wrapping her feelers around his shoulders, in an attempt to calm him. "It's okay, Dalton. Your father isn't mad at you... he's just wanting to protect you."

Under his breath, Dalton just mumbled to himself. "Some protection..."

* * *

An Umbreon sat at a computer of sorts, looking at the screen. A door hissed open from the other side of the room, a Pokemon walking in. The Umbreon turned, its blood red eyes calmly looking at the new comer. A Snivy walked in, looking slightly nervous. "I don't think its a good idea for us to meet here... what if a teacher finds out?"

The Umbreon goes and looks back at the holographic screen. "We will have plenty of time to return to our dorms if a teacher came this way. Why do you think Pak isn't with me as usual?"

"Good point... but we're still out past curfew. Why did you want to talk to me?"

"Viza. Is 'she' following the Eevee named Dalton?"

"Your brother? Yeah... Viza said that she had to stop following him for a bit, but she's watching him still. Why do you need to keep an eye on him?"

"He doesn't know it... but he'll be joining us here at IRT shortly. I just need to finish this one program, and we'll be able to tap into the memories of his partner."

"But he doesn't-"

The Umbreon went still, before shutting off the terminal, and leaping down out of the chair. "We need to leave. I would invite you into my room, but like you said, it's after curfew."

The two of them left the lab, each going to their respective rooms. A mechanical Gallade awaited the Umbreon. It 'awoke', greeting him as he walked in. [_Welcome back. Did you finish the program?_]

"No. Your warning cut us off before we could finish. We'll have to continue later. I shall see you in the morning, Pak. Goodnight."

* * *

Dalton looked out his window, at the city street below. Though it was late, he couldn't sleep, the feeling that something was watching him ever constant. Faintly, ever so faintly, he thought he could hear a voice. '_We need you... Help us._' Eyes widening, he laid down in his bed, before falling into an uneasy sleep.

* * *

**A/N: Well, this took longer than I anticipated. I'd like to credit Rueme from deviantART for the design of Nimbeon. I was contemplating making his father a Flareon, but I didn't quite like the look. I was browsing the web, when a friend from PS showed me Rueme's Drakeon Eeveelution. I found myself addicted to Nimbeon, and so here we are. Anyhow, I'll try to get the next chapter out as soon as possible, though school is going to be taking up a good bit of time, in addition to other extracurricular activities.**


End file.
